To restore, all you have to do is copy that system folder onto your /system folder. My root was acting up and kept remounting /system as ro once a second, so I needed to copy using an adb shell over USB. You may have better luck than I did with root explorer or ES.

It may be possible to just run the preinstall apk. I also had issues replacing things in /system while running, but I managed to finish the copy and reboot before the tablet shut down. If you're careful, you could probably load fastboot or something to copy while /system is not mounted.

Forth:

Tempoarily disable root and apply OTA2

Fifth:

Restore root and check that it works.

Sixth:

Temporarily disable root and apply OTA 2.5

Seventh:

Restore root and check. You should be fully updated with root.

I decided I'm going to leave the stock apps this time. We're 2 to 3 months from ICS, and I really want that update. Since Lenovo doesn't release full, signed images, it's very likely you can get in a position where you cannot update.

Copied it to an sd card and update it from the recovery menu. The tablet froze after updating (the android animation stopped) and i had to reboot it manually but it worked. iirc i did a factory reset here but i'm not sure if it was necessary.